VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 29 2019 - 20:50:31 CDT

Dallas,
  That speedup for a 2080 Ti comparing VMD 1.9.4 versions a8 vs. a31
is about what I would roughly expect at 6x the speed with the new
RTX code Turing vs. the old code on Turing. I would expect
that speedups should be larger yet if you compare vs.
previous generation Pascal or Volta hardware.

I'll have a look at that error you got in a separate email.

Best,
  John

On Tue, Apr 30, 2019 at 10:00:35AM +1000, Dallas Warren wrote:
> Can't catch a break at all ??????
>
> a8 with RTX 2080Ti 20.33 sec
> a31 with RTX 2080Ti 3.33 sec.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren_at_monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>
>
>
> On Tue, 30 Apr 2019 at 09:59, Dallas Warren <dallas.warren_at_monash.edu> wrote:
> >
> > Actually, I got those speeds wrong, apologies for that.
> >
> > a8 with RTX 2080Ti 20.33 sec
> > a31 with RTX 1080Ti 3.33 sec.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.warren_at_monash.edu
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble a nail.
> >
> >
> >
> >
> > On Tue, 30 Apr 2019 at 09:52, Dallas Warren <dallas.warren_at_monash.edu> wrote:
> > >
> > > John,
> > >
> > > In terms of rendering speed with TachyonL-OptiX, a8 with GTX 1080Ti a
> > > scene took 20.33 sec, a31 with RTX 1080Ti same scene was 3.33 sec.
> > >
> > > This is mainly for future possible use and your information, as it
> > > failed, then I restarted it and then it worked. So nothing to do
> > > right now, I will email again if the problem persists at a later date.
> > >
> > > I have just installed my RTX 2080Ti, updated the nvidia drivers,
> > > installed 1.9.4a31 and attempted to render a scene using
> > > TachyonL-OptiX(internal) of a QuickSurf with the Blownglass material.
> > > It works using a8 and fails with a31.
> > >
> > > Here is the terminal output, a8 first, followed by a31:
> > >
> > > dallas_at_morph:~/Pictures/vmd> vmd_1.9.4a8
> > > /usr/local/lib/vmd_1.9.4a8/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no
> > > version information available (required by
> > > /usr/local/lib/vmd_1.9.4a8/vmd_LINUXAMD64)
> > > Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> > > Info) http://www.ks.uiuc.edu/Research/vmd/
> > > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > > Info) Please include this reference in published work using VMD:
> > > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > > Info) -------------------------------------------------------------
> > > Info) Multithreading available, 12 CPUs detected.
> > > Info) CPU features: SSE2 AVX
> > > Info) Free system memory: 34GB (96%)
> > > Info) Creating CUDA device pool and initializing hardware...
> > > Info) Detected 1 available CUDA accelerator:
> > > Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 @ 1.63 GHz, 11GB RAM, KTO, AE3, ZCP
> > > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > > Warning) try disabling this X server option. Most OpenGL drivers
> > > Warning) disable stereoscopic display when 'Composite' is enabled.
> > > Info) OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
> > > Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> > > Info) Full GLSL rendering mode is available.
> > > Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
> > > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > > Info) Compiling 1 OptiX shaders on 1 target GPU...
> > > Info) Dynamically loaded 2 plugins in directory:
> > > Info) /usr/local/lib/vmd_1.9.4a8/plugins/LINUXAMD64/molfile
> > > after#0
> > > vmd > Info) Using plugin gro for structure file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro
> > > Info) Using plugin gro for coordinates from file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro
> > > Info) Determining bond structure from distance search ...
> > > Info) Analyzing structure ...
> > > Info) Atoms: 49203
> > > Info) Bonds: 44706
> > > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > > Info) Residues: 4497
> > > Info) Waters: 3345
> > > Info) Segments: 1
> > > Info) Fragments: 4497 Protein: 0 Nucleic: 0
> > > Info) Finished with coordinate file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro.
> > > Info) Rendering current scene to 'vmdscene.ppm' ...
> > > Info) Ambient occlusion enabled.
> > > Info) Shadow rendering enabled.
> > > OptiXDisplayDevice) Total rendering time: 20.23 sec
> > > Info) Executing post-render cmd 'display vmdscene.ppm' ...
> > > Info) Rendering complete.
> > > Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> > > Info) Exiting normally.
> > >
> > > dallas_at_morph:~/Pictures/vmd> vmd_1.9.4a31
> > > /usr/local/lib/vmd_1.9.4a31/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no
> > > version information available (required by
> > > /usr/local/lib/vmd_1.9.4a31/vmd_LINUXAMD64)
> > > Info) VMD for LINUXAMD64, version 1.9.4a31 (March 13, 2019)
> > > Info) http://www.ks.uiuc.edu/Research/vmd/
> > > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > > Info) Please include this reference in published work using VMD:
> > > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > > Info) -------------------------------------------------------------
> > > Info) Multithreading available, 12 CPUs detected.
> > > Info) CPU features: SSE2 AVX
> > > Info) Free system memory: 34GB (95%)
> > > Info) Creating CUDA device pool and initializing hardware...
> > > Info) Detected 1 available CUDA accelerator:
> > > Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 1.63 GHz, 11GB RAM, KTO, AE3, ZCP
> > > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > > Warning) try disabling this X server option. Most OpenGL drivers
> > > Warning) disable stereoscopic display when 'Composite' is enabled.
> > > Info) OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
> > > Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> > > Info) Full GLSL rendering mode is available.
> > > Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
> > > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > > Info) Compiling 1 OptiX shaders on 1 target GPU...
> > > Info) Dynamically loaded 3 plugins in directory:
> > > Info) /usr/local/lib/vmd_1.9.4a31/plugins/LINUXAMD64/molfile
> > > after#0
> > > vmd > Info) Using plugin gro for structure file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro
> > > Info) Using plugin gro for coordinates from file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro
> > > Info) Determining bond structure from distance search ...
> > > Info) Analyzing structure ...
> > > Info) Atoms: 49203
> > > Info) Bonds: 44706
> > > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > > Info) Residues: 4497
> > > Info) Waters: 3345
> > > Info) Segments: 1
> > > Info) Fragments: 4497 Protein: 0 Nucleic: 0
> > > Info) Finished with coordinate file
> > > /home/dallas/experiments/current/19-034/run_files/md_0.gro.
> > > CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu line 1402
> > > CUDA Thrust sort_by_key() failed: CUDASort.cu line 190
> > > dev_radix_sort_by_key() failed: CUDASpatialSearch.cu line 259
> > > Info) Rendering current scene to 'vmdscene.ppm' ...
> > > Info) Ambient occlusion enabled.
> > > Info) Shadow rendering enabled.
> > > Segmentation fault (core dumped)
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Drug Delivery, Disposition and Dynamics
> > > Monash Institute of Pharmaceutical Sciences, Monash University
> > > 381 Royal Parade, Parkville VIC 3052
> > > dallas.warren_at_monash.edu
> > > ---------------------------------
> > > When the only tool you own is a hammer, every problem begins to resemble a nail.
> > >
> > > On Tue, 26 Feb 2019 at 14:40, John Stone <johns_at_ks.uiuc.edu> wrote:
> > > >
> > > > Hi,
> > > > Now that the NVIDIA drivers with RTX support are generally
> > > > available, I have made a current 64-bit Linux test build of VMD 1.9.4 (a29)
> > > > that includes RTX hardware-accelerated ray tracing, and it is
> > > > posted on the web site. To use this version you will need the latest
> > > > NVIDIA 418.xx (where xx >= 30) driver version from the NVIDIA web site.
> > > >
> > > > VMD users should expect TachyonLOPtiX ray tracing performance gains
> > > > that range as high as 8x faster when comparing the new RTX GPUs with
> > > > the new VMD with prior versions of VMD running on so-called
> > > > Pascal and Volta class NVIDIA GPUs.
> > > >
> > > > Best regards,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > --
> > > > NIH Center for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > > > http://www.ks.uiuc.edu/Research/vmd/
> > > > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/